In the course of studying a nonconditional polymerase mutant of B-tropic MuLV, we have found that enzyme pausing correlates with the presence of certain consensus sequences within multibranch loop structures. The pol mutant which synthesizes a truncated reverse transcriptase molecule is able to initiate reverse transcription and transfer from the 5' to the 3' end of genomic RNA but cannot read past one of the pause sites. Thus, the mutant terminates synthesis prematurely. The mutation in the pol gene has been sequenced and consists of the addition of one C residue to a 5 bp stretch of Cs. This addition results in immediate termination of translation since a TGA codon is brought immediately into frame. Analysis of this result in light of phenotypic characterization of the mutant allows us to conclude that the MuLV pol gene contains coding capacity for a protein of about 13 K daltons upstream of reverse transcriptase and a protein of about 40K daltons downstream of the polymerase coding region and that the RNase H and DNA polymerase active sites are located in the N-terminal two-thirds of the reverse transcriptase molecule. In addition, we have determined the DNA sequence of 1.8 Kb from the 5' end of two molecularly cloned sarcoma viruses which either do (M1 MSV) or do not (HT1 MSV) produce virion structural proteins encoded in the 5' portion of the genome. We have shown that the primary differences occur in the 5' untranslated portion of the genome.